How To Process Data From Bisulfite Sequencing Of An Exome

Question

[kanwarjag]

I have an exome sequencing data and wonder what should be the best way to process these file for bisulfite seq. I believe I can align with BWA but how can I determine the methylation status.

Thanks

Answer 1

[Devon Ryan]

You don't want to use BWA, the results will be crap. Use bismark or bison (the former is easier to setup and more flexible, the latter faster and more accurate).

[Charles Warden]

Bismark also has Perl scripts that allow you to calculate percentage methylation values (beyond just doing the alignment).

Presumably, you will also want to find differentially methylated regions. I would recommend using methylKit for this, but you can also use COHCAP since it looks like you used a targeted BS-Seq library:

http://sourceforge.net/projects/cohcap/

http://www.ncbi.nlm.nih.gov/pubmed/23598999

BTW, COHCAP also has a Bioconductor version (but it is a devel release). Feel free to try that if it helps:

http://bioconductor.org/packages/devel/bioc/html/COHCAP.html

Answer 2

[Matt Shirley]

You don't want to use BWA on its own, as you want to align your bisulfite treated reads against an in-silico bisulfite treated genome. You will also want a script that summarizes methylation from the alignments. Aside from bismark and bison you should look at the neat BWA-meth wrapper that brentp recently published on Arxiv.